- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.60 Å
- Oligo State
- homo-dimer
- Ligands
- 6 x JPE: [(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-pyridin-3-yl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-3-oxidanyl-propanoyl]sulfamate(Non-covalent)
- 4 x CL: CHLORIDE ION(Non-functional Binders)
- 6 x SO4: SULFATE ION(Non-functional Binders)
SO4.6: 3 residues within 4Å:- Chain A: N.120, V.121, E.122
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:E.122
- Water bridges: A:N.120
SO4.7: 3 residues within 4Å:- Chain A: R.354, E.355, R.397
3 PLIP interactions:3 interactions with chain A- Water bridges: A:E.355
- Salt bridges: A:R.354, A:R.397
SO4.8: 2 residues within 4Å:- Chain A: R.324, T.352
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:T.352, A:T.352
- Salt bridges: A:R.324
SO4.24: 3 residues within 4Å:- Chain B: N.120, V.121, E.122
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:E.122
- Water bridges: B:N.120
SO4.25: 3 residues within 4Å:- Chain B: R.354, E.355, R.397
3 PLIP interactions:3 interactions with chain B- Water bridges: B:E.355
- Salt bridges: B:R.354, B:R.397
SO4.26: 2 residues within 4Å:- Chain B: R.324, T.352
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:T.352, B:T.352
- Salt bridges: B:R.324
- 8 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
DMS.9: 6 residues within 4Å:- Chain A: W.126, G.127, T.128, G.320, P.322
- Ligands: EDO.14
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:T.128
DMS.10: 6 residues within 4Å:- Chain A: F.179, D.182, L.183, E.186, Q.187, Y.422
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:Y.422
- Salt bridges: A:E.186
DMS.11: 6 residues within 4Å:- Chain A: R.130, N.405, Y.406, Q.408, E.414
- Ligands: EDO.14
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:Q.408
- Salt bridges: A:E.414
DMS.12: 5 residues within 4Å:- Chain A: Q.168, R.171, M.423, N.424, L.426
No protein-ligand interaction detected (PLIP)DMS.27: 6 residues within 4Å:- Chain B: W.126, G.127, T.128, G.320, P.322
- Ligands: EDO.32
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:T.128
- Water bridges: B:T.128
DMS.28: 6 residues within 4Å:- Chain B: F.179, D.182, L.183, E.186, Q.187, Y.422
2 PLIP interactions:2 interactions with chain B- Water bridges: B:Y.422
- Salt bridges: B:E.186
DMS.29: 6 residues within 4Å:- Chain B: R.130, N.405, Y.406, Q.408, E.414
- Ligands: EDO.32
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:Q.408
- Salt bridges: B:E.414
DMS.30: 5 residues within 4Å:- Chain B: Q.168, R.171, M.423, N.424, L.426
No protein-ligand interaction detected (PLIP)- 10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.13: 10 residues within 4Å:- Chain A: V.163, M.165, H.173, L.281, Q.286, F.287, D.288, G.396
- Chain B: Y.194
- Ligands: JPE.1
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:H.173, A:Q.286, A:D.288, A:G.396
EDO.14: 6 residues within 4Å:- Chain A: G.320, P.322, N.405, Y.406
- Ligands: DMS.9, DMS.11
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:Y.406
- Water bridges: A:N.405
EDO.15: 5 residues within 4Å:- Chain A: P.4, L.7, R.8, E.34, I.96
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:E.34
EDO.16: 6 residues within 4Å:- Chain A: N.200, Q.201, D.228, T.229, S.230, N.231
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:Q.201, A:D.228, A:N.231
- Water bridges: A:N.200, A:D.202
EDO.17: 3 residues within 4Å:- Chain A: H.188, H.311, K.314
1 PLIP interactions:1 interactions with chain A- Water bridges: A:H.311
EDO.31: 10 residues within 4Å:- Chain A: Y.194
- Chain B: V.163, M.165, H.173, L.281, Q.286, F.287, D.288, G.396
- Ligands: JPE.19
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:H.173, B:Q.286, B:D.288, B:G.396
EDO.32: 6 residues within 4Å:- Chain B: G.320, P.322, N.405, Y.406
- Ligands: DMS.27, DMS.29
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:Y.406
- Water bridges: B:N.405
EDO.33: 5 residues within 4Å:- Chain B: P.4, L.7, R.8, E.34, I.96
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:E.34
EDO.34: 6 residues within 4Å:- Chain B: N.200, Q.201, D.228, T.229, S.230, N.231
5 PLIP interactions:5 interactions with chain B- Hydrogen bonds: B:Q.201, B:D.228, B:N.231
- Water bridges: B:N.200, B:D.202
EDO.35: 3 residues within 4Å:- Chain B: H.188, H.311, K.314
1 PLIP interactions:1 interactions with chain B- Water bridges: B:H.311
- 2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)
TRS.18: 5 residues within 4Å:- Chain A: P.421, Y.422
- Chain B: P.421, Y.422
- Ligands: TRS.36
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:P.421
- Water bridges: A:D.182, A:Y.422
TRS.36: 5 residues within 4Å:- Chain A: P.421, Y.422
- Chain B: P.421, Y.422
- Ligands: TRS.18
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:P.421
- Water bridges: B:D.182, B:D.182
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Cain, R. et al., Structure-Guided Enhancement of Selectivity of Chemical Probe Inhibitors Targeting Bacterial Seryl-tRNA Synthetase. J.Med.Chem. (2019)
- Release Date
- 2020-01-22
- Peptides
- Serine--tRNA ligase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.60 Å
- Oligo State
- homo-dimer
- Ligands
- 6 x JPE: [(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-2-pyridin-3-yl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-3-oxidanyl-propanoyl]sulfamate(Non-covalent)
- 4 x CL: CHLORIDE ION(Non-functional Binders)
- 6 x SO4: SULFATE ION(Non-functional Binders)
- 8 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
- 10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Cain, R. et al., Structure-Guided Enhancement of Selectivity of Chemical Probe Inhibitors Targeting Bacterial Seryl-tRNA Synthetase. J.Med.Chem. (2019)
- Release Date
- 2020-01-22
- Peptides
- Serine--tRNA ligase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
A